Implemented calculation of unique crystal contacts
Now hetatoms can be filtered by size when calculating ASAs in interfaces
Improved HETATOMs filtering for interface ASA calculation
Some refactoring and improvement of docs
Added unit test for CrystalBuilder and fixed some docs
Introduced a more general interface-between-2-molecules representation
Now ChainInterface/List became StructureInterface/List and are moved to
contacts package. Other kind of interfaces between 2 molecules or
submolecules (e.g. between domains) can be handled with this
representation.
Merge pull request #158 from josemduarte/master

New feature: reconstruction of crystal from AU and calculation of unique interfaces in crystal
#156 adding missing fields
#156 adding missing fields
Introducing slf4j #155
- added runTime scope binding for log4j2 since it's the one logger
framework that was used already elsewhere. We even had already some
config files for it in the structure module
- added the safe config to all poms of modules. Config files for log4j2
are only in the structure module. Other modules will have to add config
files if needed
- default level in config files set to: warn for run, info for test
- moved logging in the PDB parser to slf4j
Fixed issue: wasn't pointing to the right class in logger
Merge pull request #159 from josemduarte/master

Introducing slf4j #155
Some fixes for #111 and #155
Default log4j config now outputs to stderr
Important fix for #155, was not specifying runtime scope correctly
More on #155 and #111
Convert SimpleMMcifParser to use SLF4J logging